Variant report

Variant	rs2535294
Chromosome Location	chr6:31062133-31062134
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30780845..30782405-chr6:31060991..31063180,2	K562	blood:
2	chr6:30701308..30703413-chr6:31060856..31063680,2	MCF-7	breast:
3	chr6:31060052..31062667-chr6:31078284..31080842,2	MCF-7	breast:
4	chr6:31053892..31056272-chr6:31061858..31063779,2	K562	blood:

Variant related genes	Relation type
ENSG00000204542	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1064190	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1064191	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1265046	0.87[EUR][1000 genomes]
rs1265052	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1265053	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1265054	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1265055	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1265056	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1265057	0.81[AMR][1000 genomes]
rs1265058	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1265059	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1265060	0.81[AMR][1000 genomes]
rs1265063	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1265064	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2233966	0.88[EUR][1000 genomes]
rs2394417	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2429721	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2429723	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2508013	0.89[AFR][1000 genomes]
rs2517410	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2517414	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2517423	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2517427	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2517440	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2517443	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2517450	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2517452	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2517453	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2517455	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2517458	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2517460	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2517464	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2517465	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2517469	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2517470	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2517529	0.81[AFR][1000 genomes]
rs2517541	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2517556	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2523860	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2535277	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2535279	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2535282	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2535283	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2535287	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2535288	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2535289	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2535290	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2535291	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2535292	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2535293	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2535295	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2535297	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2535299	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2535300	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2535301	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2535302	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2535303	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2535310	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3095305	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3130546	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3130548	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3130956	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3130957	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3130958	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3130959	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3130960	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3130961	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3130962	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3130963	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3130964	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3130966	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3130970	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7381897	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7383281	0.81[AMR][1000 genomes]
rs9263493	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9263494	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9263593	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9263597	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9263602	0.81[AMR][1000 genomes]
rs9263626	0.81[AFR][1000 genomes]
rs9263627	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9263628	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9263629	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9263631	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
11	nsv462746	chr6:31060162-31082361	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv601489	chr6:31060162-31082361	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2535294	HCG22	cis	lymphoblastoid	seeQTL
rs2535294	HCG22	cis	Lymphoblastoid	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31040600-31062400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr6:31051000-31062200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:31055200-31062200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:31055400-31062400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:31058800-31066400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:31059800-31062200	Weak transcription	Gastric	stomach
7	chr6:31059800-31063000	Enhancers	HepG2	liver
8	chr6:31060200-31062600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:31060600-31062200	Enhancers	HUVEC	blood vessel
10	chr6:31060600-31065200	Enhancers	Primary hematopoietic stem cells	blood
11	chr6:31060800-31062800	Enhancers	A549	lung
12	chr6:31060800-31063200	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr6:31060800-31066800	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr6:31061000-31062200	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr6:31061000-31062600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:31061000-31063000	Enhancers	Brain Substantia Nigra	brain
17	chr6:31061000-31063800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr6:31061000-31065800	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr6:31061200-31064800	Weak transcription	K562	blood
20	chr6:31061600-31063200	Enhancers	Primary B cells from cord blood	blood
21	chr6:31061600-31063200	Enhancers	Primary B cells from peripheral blood	blood
22	chr6:31061600-31065600	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr6:31061600-31065600	Enhancers	Primary T cells fromperipheralblood	blood
24	chr6:31061800-31062400	Bivalent Enhancer	Placenta	Placenta
25	chr6:31061800-31062600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr6:31061800-31062800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:31061800-31062800	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr6:31061800-31063000	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr6:31061800-31063000	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr6:31061800-31063200	Enhancers	Brain Anterior Caudate	brain
31	chr6:31061800-31063200	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr6:31061800-31063600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:31061800-31066000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr6:31062000-31062200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr6:31062000-31062200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:31062000-31062400	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr6:31062000-31062400	Enhancers	Duodenum Mucosa	Duodenum
38	chr6:31062000-31062400	Enhancers	HSMM	muscle
39	chr6:31062000-31062600	Enhancers	Fetal Muscle Leg	muscle
40	chr6:31062000-31062800	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr6:31062000-31062800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr6:31062000-31062800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:31062000-31062800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:31062000-31062800	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr6:31062000-31062800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:31062000-31062800	Enhancers	Colonic Mucosa	Colon
47	chr6:31062000-31062800	Enhancers	Fetal Muscle Trunk	muscle
48	chr6:31062000-31062800	Enhancers	Lung	lung
49	chr6:31062000-31062800	Enhancers	Right Atrium	heart
50	chr6:31062000-31063000	Enhancers	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links